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Re: Restraining a disulphide bridge



Hi Marc!

Did you redefine the special_patches routine, i.e. write into your top
script:

INCLUDE SET ALNFILE = '1fep.ali'
SET KNOWNS = '1fep_xr'
SET SEQUENCE ='1fep_ok'
SET ATOM_FILES_DIRECTORY = '.'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 10
SET DEVIATION = 2.0
SET RAND_SEED = -12312
CALL ROUTINE = 'model'
STOP

... and then:

SUBROUTINE ROUTINE = 'special_patches'
    PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494'
    RETURN
END_SUBROUTINE


I hope this will work.

Nice greetings,


Andreas

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On Tue, 11 Sep 2001, Marc BAADEN wrote:

>
> Dear Professor Sali,
>
> although I tried to thoroughly read through your documentation,
> and found several references (and examples) to patching disulphide
> bridges, I could not get it to work for my particular case.
>
> I tried to use Modeller v6a (but we also have Modeller4 in the lab,
> if that would make any difference).
>
> My case might be a bit special:
> I have got an Xray structure, with missing sidechains+residues.
> One Cysteine is present, the second missing, There are only 2 in
> the structure, and there has to be a disulphide bridge between
> them.
>
> I only need a homology model where missing residues and sidechains
> are completed. So my usual modeller script looks like this:
>
> INCLUDE
> SET ALNFILE = '1fep.ali'
> SET KNOWNS = '1fep_xr'
> SET SEQUENCE = '1fep_ok'
> SET ATOM_FILES_DIRECTORY = '.'
> SET STARTING_MODEL = 1
> SET ENDING_MODEL = 10
> SET DEVIATION = 2.0
> SET RAND_SEED = -12312
> CALL ROUTINE = 'model'
>
> Using xray coordinates from 1fep_xr.atm.
>
> Now I wanted to add something like
>
> PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494'
>
> which leads to an error of
> Run READ_TOPOLOGY and GENERATE_TOPOLOGY first.
>
> Now I wonder, is this the right way to add my disulphide restraint ?
> If yes, then what kind of topology should I use and how ?
> Do I need to build an initial complete model first, and my 10 models
> afterwards ?
>
> Thank you very much in advance,
>
> Best wishes,
>
>   Marc Baaden
>
> --
>  Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
>  ">mailto:  - ICQ# 11466242 -  http://www.marc-baaden.de
>  FAX/Voice +49 40333 968508  -  Tel: +44 1865 275380  or  +33 609 843217
>
>